STONY BROOK MEDICINE

Department of Biomedical Informatics

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Alisa Yurovsky

Department of Biomedical Informatics

Publications

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RankByGene: GeneGene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency

Wentao Huang, Meilong Xu, Xiaoling Hu, Shahira Abousamra, Aniruddha Ganguly, Saarthak Kapse, Alisa Yurovsky, Prateek Prasanna, Tahsin Kurç, Joel Saltz, Michael L. Miller, Chao Chen

ORCID match IEEE Transactions on Medical Imaging · 2026 · Found in OpenAlex

DOI: 10.1109/tmi.2026.3725898

Choose for “RankByGene: GeneGene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency”

Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer

Brian Nelson, Lyanne A. Delgado-Coka, Н. В. Марченко, Luisa F. Escobar‐Hoyos, Kenneth R Shroyer, Alisa Yurovsky, Trey Ideker, Gábor Balázsi, Thomas MacCarthy, Scott Powers

ORCID match Molecular Oncology · 2026 · Found in OpenAlex, PubMed

DOI: 10.1002/1878-0261.70218

Choose for “Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer”

Author response for "Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer"

Brian Nelson, Lyanne A. Delgado-Coka, Natalia Marchenko, Luisa F. Escobar‐Hoyos, Kenneth R Shroyer, Alisa Yurovsky, Trey Ideker, Gábor Balázsi, Thomas MacCarthy, Scott Powers

ORCID match · 2026 · Found in OpenAlex

DOI: 10.1002/1878-0261.70218/v2/response1

Choose for “Author response for "Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer"”

MERGE: Multi-faceted Hierarchical Graph-based GNN for Gene Expression Prediction from Whole Slide Histopathology Images

Aniruddha Ganguly, Debolina Chatterjee, Wentao Huang, Jie Zhang, Alisa Yurovsky, Travis S. Johnson, Chao Chen

ORCID match Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition · 2025 · Found in OpenAlex, PubMed

DOI: 10.1109/cvpr52734.2025.01455

Choose for “MERGE: Multi-faceted Hierarchical Graph-based GNN for Gene Expression Prediction from Whole Slide Histopathology Images”

DeepVRegulome: DNABERT-based deep-learning framework for predicting the functional impact of short genomic variants on the human regulome

Pratik Dutta, Matthew B. Obusan, Rekha Sathian, Max Chao, Pallavi Surana, Nimisha Papineni, Yanrong Ji, Zhi Quan Zhou, Han Liu, Alisa Yurovsky, Ramana V. Davuluri

ORCID match ArXiv.org · 2025 · Found in OpenAlex

DOI: 10.48550/arxiv.2511.09026

Choose for “DeepVRegulome: DNABERT-based deep-learning framework for predicting the functional impact of short genomic variants on the human regulome”

A graded neonatal mouse model of necrotizing enterocolitis demonstrates that mild enterocolitis is sufficient to activate microglia and increase cerebral cytokine expression.

Cuilee Sha, Trevor Van Brunt, Jacob Kudria, Donna Schmidt, Alisa Yurovsky, Jela Bandovic, Michael Giarrizzo, Joyce Lin, Styliani-Anna Tsirka, Agnieszka B Bialkowska, Lonnie P Wollmuth, Esther M Speer, Helen Hsieh

Name match · unconfirmed PloS one · 2025 · Found in PubMed

DOI: 10.1371/journal.pone.0323626

Choose for “A graded neonatal mouse model of necrotizing enterocolitis demonstrates that mild enterocolitis is sufficient to activate microglia and increase cerebral cytokine expression.”

RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency

Wentao Huang, Meilong Xu, Hu, Xiaoling, Shahira Abousamra, Aniruddha Ganguly, Saarthak Kapse, Alisa Yurovsky, Prateek Prasanna, Tahsin Kurç, Joel Saltz, M. L. Miller, Chao Chen

ORCID match arXiv (Cornell University) · 2024 · Found in OpenAlex

DOI: 10.48550/arxiv.2411.15076

Choose for “RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency”

New Spatial Phenotypes from Imaging Uncover Survival Differences for Breast Cancer Patients

Mahmudul Hasan, Ariadna Kim Silva, Shahira Abousamra, Shao‐Jun Tang, Prateek Prasanna, Joel Saltz, Kevin Gardner, Chao Chen, Alisa Yurovsky

ORCID match ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2024 · Found in OpenAlex, PubMed

DOI: 10.1145/3698587.3701333

Choose for “New Spatial Phenotypes from Imaging Uncover Survival Differences for Breast Cancer Patients”

Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria

Nuri K. Hegelmeyer, Mary Lou Previti, Joshua Andrade, Raditya Utama, Richard Sejour, Justin Gardin, Stéphanie Muller, Steven Ketchum, Alisa Yurovsky, Bruce Futcher, Sara Goodwin, Beatrix Ueberheide, Jessica C. Seeliger

ORCID match bioRxiv (Cold Spring Harbor Laboratory) · 2023 · Found in OpenAlex, PubMed

DOI: 10.1101/2023.03.17.532606

Choose for “Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria”

Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria

Nuri K. Hegelmeyer, Lia A. Parkin, Mary Lou Previti, Joshua Andrade, Raditya Utama, Richard Sejour, Justin Gardin, Stéphanie Muller, Steven Ketchum, Alisa Yurovsky, Bruce Futcher, Sara Goodwin, Beatrix Ueberheide, Jessica C. Seeliger

ORCID match mBio · 2023 · Found in OpenAlex, PubMed

DOI: 10.1128/mbio.00841-23

Choose for “Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria”

FaStaNMF: A Fast and Stable Non-Negative Matrix Factorization for Gene Expression

M. D. Sweeney, Luke A. Torre-Healy, Virginia L. Ma, Margaret A Hall, Lucie Chrastecka, Alisa Yurovsky, Richard A. Moffitt

ORCID match IEEE Transactions on Computational Biology and Bioinformatics · 2023 · Found in OpenAlex

DOI: 10.1109/tcbb.2023.3296979

Choose for “FaStaNMF: A Fast and Stable Non-Negative Matrix Factorization for Gene Expression”

Statistical methodology for ribosomal frameshift detection

Alisa Yurovsky, Justin Gardin, Bruce Futcher, Steven Skiena

ORCID match ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2022 · Found in OpenAlex, PubMed

DOI: 10.1145/3535508.3545529

Choose for “Statistical methodology for ribosomal frameshift detection”

Session details: Systems biology

Alisa Yurovsky

ORCID match · 2022 · Found in OpenAlex

DOI: 10.1145/3552472

Choose for “Session details: Systems biology”

No Ramp Needed: Spandrels, Statistics, and a Slippery Slope

Richard Sejour, Janet Leatherwood, Alisa Yurovsky, Bruce Futcher

ORCID match bioRxiv (Cold Spring Harbor Laboratory) · 2022 · Found in OpenAlex

DOI: 10.1101/2022.06.27.497802

Choose for “No Ramp Needed: Spandrels, Statistics, and a Slippery Slope”

METHODOLOGY AND REGULATORY IMPLICATIONS OF ECG DATABASE FORMATION FOR TESTING AUTOMATED ALGORITHMS AND ARTIFICIAL INTELLIGENCE SYSTEMS

D. V. Shutov, Д. В. Дроздов, Tamara M. Gazashvili, A A Popov, V. P. Efimova, А. Ф. Сафарова, V Yurtaeva, Ekaterina V. Shutova, A.E. Demkina, D.A. Prilutsky, Alisa Yurovsky, А. С. Шкода, С. П. Морозов

ORCID match Vrach i informacionnye tehnologii · 2021 · Found in OpenAlex

DOI: 10.25881/18110193-2021-4-4

Choose for “METHODOLOGY AND REGULATORY IMPLICATIONS OF ECG DATABASE FORMATION FOR TESTING AUTOMATED ALGORITHMS AND ARTIFICIAL INTELLIGENCE SYSTEMS”

Pre-Phaser

Alisa Yurovsky, Bruce Futcher, Steven Skiena

ORCID match · 2019 · Found in OpenAlex

DOI: 10.1145/3307339.3342174

Choose for “Pre-Phaser”

DeepAnnotator

Mohammad Ruhul Amin, Alisa Yurovsky, Yingtao Tian, Steven Skiena

ORCID match · 2018 · Found in OpenAlex

DOI: 10.1145/3233547.3233577

Choose for “DeepAnnotator”

Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing

María Gutiérrez‐Arcelus, Halit Ongen, Tuuli Lappalainen, Stephen B. Montgomery, Alfonso Buil, Alisa Yurovsky, Julien Bryois, Ismaël Padioleau, Luciana Romano, Alexandra Planchon, Emilie Falconnet, Deborah Bielser, Maryline Gagnebin, Thomas Giger, Christelle Borel, Audrey Letourneau, Periklis Makrythanasis, Michel Guipponi, Corinne Gehrig, Stylianos E. Antonarakis, Emmanouil T. Dermitzakis

ORCID match PLoS Genetics · 2015 · Found in OpenAlex

DOI: 10.1371/journal.pgen.1004958

Choose for “Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing”

Reply to Simmonds et al.: Codon pair and dinucleotide bias have not been functionally distinguished

Bruce Futcher, Oleksandr Gorbatsevych, Sam H. Shen, Charles B. Stauft, Yutong Song, Bingyin Wang, Janet Leatherwood, Justin Gardin, Alisa Yurovsky, Steffen Mueller, Eckard Wimmer

ORCID match Proceedings of the National Academy of Sciences · 2015 · Found in OpenAlex, PubMed

DOI: 10.1073/pnas.1507710112

Choose for “Reply to Simmonds et al.: Codon pair and dinucleotide bias have not been functionally distinguished”

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

Sebastian M. Waszak, Olivier Delaneau, Andreas R. Gschwind, Helena Kilpinen, Sunil K. Raghav, Robert M. Witwicki, Andrea Orioli, Michael R. Wiederkehr, Nikolaos I. Panousis, Alisa Yurovsky, Luciana Romano-Palumbo, Alexandra Planchon, Deborah Bielser, Ismaël Padioleau, Gilles Udin, Sarah Thurnheer, David L. Hacker, Nouria Hernandez, Alexandre Reymond, Bart Deplancke, Emmanouil T. Dermitzakis

ORCID match Cell · 2015 · Found in OpenAlex

DOI: 10.1016/j.cell.2015.08.001

Choose for “Population Variation and Genetic Control of Modular Chromatin Architecture in Humans”

Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference

Sam H. Shen, Charles B. Stauft, Oleksandr Gorbatsevych, Yutong Song, Charles B. Ward, Alisa Yurovsky, Steffen Mueller, Bruce Futcher, Eckard Wimmer

ORCID match Proceedings of the National Academy of Sciences · 2015 · Found in OpenAlex

DOI: 10.1073/pnas.1502864112

Choose for “Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference”

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

María Gutiérrez‐Arcelus, Tuuli Lappalainen, Stephen B. Montgomery, Alfonso Buil, Halit Ongen, Alisa Yurovsky, Julien Bryois, Thomas Giger, Luciana Romano, Alexandra Planchon, Emilie Falconnet, Deborah Bielser, Maryline Gagnebin, Ismaël Padioleau, Christelle Borel, Audrey Letourneau, Periklis Makrythanasis, Michel Guipponi, Corinne Gehrig, Stylianos E. Antonarakis, Emmanouil T. Dermitzakis

ORCID match eLife · 2013 · Found in OpenAlex

DOI: 10.7554/elife.00523

Choose for “Passive and active DNA methylation and the interplay with genetic variation in gene regulation”

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

Sebastian M. Waszak, Helena Kilpinen, Andreas R. Gschwind, Andrea Orioli, Sunil K. Raghav, Robert M. Witwicki, Eugenia Migliavacca, Alisa Yurovsky, Tuuli Lappalainen, Nouria Hernandez, Alexandre Reymond, Emmanouil T. Dermitzakis, Bart Deplancke

ORCID match Bioinformatics · 2013 · Found in OpenAlex

DOI: 10.1093/bioinformatics/btt667

Choose for “Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data”

Correction: Passive and active DNA methylation and the interplay with genetic variation in gene regulation

María Gutiérrez‐Arcelus, Tuuli Lappalainen, Stephen B. Montgomery, Alfonso Buil, Halit Ongen, Alisa Yurovsky, Julien Bryois, Thomas Giger, Luciana Romano, Alexandra Planchon, Emilie Falconnet, Deborah Bielser, Maryline Gagnebin, Ismaël Padioleau, Christelle Borel, Audrey Letourneau, Periklis Makrythanasis, Michel Guipponi, Corinne Gehrig, Stylianos E. Antonarakis, Emmanouil T. Dermitzakis

ORCID match eLife · 2013 · Found in OpenAlex

DOI: 10.7554/elife.01045

Choose for “Correction: Passive and active DNA methylation and the interplay with genetic variation in gene regulation”

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

Helena Kilpinen, Sebastian M. Waszak, Andreas R. Gschwind, Sunil K. Raghav, Robert M. Witwicki, Andrea Orioli, Eugenia Migliavacca, Michael R. Wiederkehr, María Gutiérrez‐Arcelus, Nikolaos I. Panousis, Alisa Yurovsky, Tuuli Lappalainen, Luciana Romano-Palumbo, Alexandra Planchon, Deborah Bielser, Julien Bryois, Ismaël Padioleau, Gilles Udin, Sarah Thurnheer, David L. Hacker, Leighton J. Core, John T. Lis, Nouria Hernandez, Alexandre Reymond, Bart Deplancke, Emmanouil T. Dermitzakis

ORCID match Science · 2013 · Found in OpenAlex

DOI: 10.1126/science.1242463

Choose for “Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription”

Author response: Passive and active DNA methylation and the interplay with genetic variation in gene regulation

María Gutiérrez‐Arcelus, Tuuli Lappalainen, Stephen B. Montgomery, Alfonso Buil, Halit Ongen, Alisa Yurovsky, Julien Bryois, Thomas Giger, Luciana Romano, Alexandra Planchon, Emilie Falconnet, Deborah Bielser, Maryline Gagnebin, Ismaël Padioleau, Christelle Borel, Audrey Letourneau, Periklis Makrythanasis, Michel Guipponi, Corinne Gehrig, Stylianos E. Antonarakis, Emmanouil T. Dermitzakis

ORCID match · 2013 · Found in OpenAlex

DOI: 10.7554/elife.00523.024

Choose for “Author response: Passive and active DNA methylation and the interplay with genetic variation in gene regulation”
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